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Inferring Epigenetic and Genetic Biomarkers of cancer in cell-free DNA

ABSTRACT: Inferring Epigenetic and Genetic Biomarkers of cancer in cell-free DNA

PROVIDER: PRJNA562656 | ENA |

REPOSITORIES: ENA

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Inferring Epigenetic and Genetic Biomarkers of cancer in cell-free DNA

Project description:Aims: Cancer is an important public health problem worldwide. In recent years, methods based on the analysis of plasma cfDNA which is as an emerging technology have been largely explored for noninvasive prenatal testing and cancer liquid biopsy. We inferred both epigenetic and genetic biomarkers of esophageal cancer (ESCA) in cfDNA with adapted SALP-seq. Materials & methods: Next Generation Sequencing libraries of cfDNA samples from ESCA patients and healthy people were constructed by using SALP-seq. We performed bioinformatics analysis on our sequencing data to find cancer-specific biomarkers. Results & conclusion: 54 important regulatory elements of ESCA, 49 epigenetic and 37 genetic ESCA-specific genes were inferred in cfDNA with SALP-seq, which may ultimately contribute to the development of effective diagnostic and therapeutic approaches for ESCA.

2022-08-28 | GSE136541 | GEO

Epigenetic Biomarkers of Aging

Project description:Epigenetic Biomarkers of Aging

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DNA 5-hydroxymethylcytosines from cell-free circulating DNA as diagnostic biomarkers for human cancers

Project description:DNA modifications such as 5-methylcytosines (5mC) and 5-hydroxymethylcytosines (5hmC) are epigenetic marks known to affect global gene expression in mammals. Given their prevalence in the human genome, close correlation with gene expression, and high chemical stability, these DNA epigenetic marks could serve as ideal biomarkers for cancer diagnosis. Taking advantage of a highly sensitive and selective chemical labeling technology, we report here genome-wide 5hmC profiling in circulating cell-free DNA (cfDNA) and paired tumor/adjacent tissues collected from a cohort of 90 healthy individuals and 260 patients recently diagnosed with colorectal, gastric, pancreatic, liver, or thyroid cancer. 5hmC was mainly distributed in transcriptionally active regions coincident with open chromatin and permissive histone modifications. Robust cancer-specific epigenetic signatures in cfDNA were identified in different cancers. 5hmC-based biomarkers demonstrated highly accurate predictive value for patients with colorectal and gastric cancers versus healthy controls, superior to conventional biomarkers, and comparable to epigenetic biomarkers from tissue biopsies. This new strategy could lead to the development of an effective blood-based, minimally-invasive cancer diagnosis and prognosis approach.

2017-09-05 | GSE89570 | GEO

Genetic and Epigenetic Determinants of Response to Fluorouracil-based Adjuvant Chemotherapy in Patients With Stage III Colorectal Cancer

Project description:The goal of this laboratory research is to look for genetic and epigenetic markers that can predict which patients with stage III colorectal cancer will benefit from fluorouracil-based adjuvant chemotherapy.

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Genetic Susceptibility and Biomarkers of Platinum-Related Toxicities

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